Anyway, I would think something older than TMNT, come on. How about BERZERK? Maybe in a 3D maze, FPS style or something? Or how about a really cool 3D JOUST? Hmmm, that sounds fun.
Other picks: Jungle Hunt, Moon Patrol, Zaxxon, Defender, etc.
I would say TRON, but there's a new TRON game in the works that looks killer. 
Well the trouble with old games and 3d is that it doesn't work. Most, if not all of the commercial retrogame to 3d conversions have, well, sucked --I'm attempting to get by the auto-censor and should be beaten after I re-read the rules--. Think about it... they made a 3d millipede, it sucked. They made a 3d pacman.. it was ok but sorta lame. They made a 3d frogger which actually plays pretty good, but it doesn't remind me of the original frogger at all save the first level. I believe there is already a 3d jousting game, although it's not joust. But reagardless of that... the really really old games don't have enough gameplay to be translated to 3d. Think about it... all of jousts levels looked alike and played alike.... that could get real old on a brand new game. Same with moon patrol... it's a very small game and would be hard to expand upon. They have a 3d jungle hunt.... it's called tarzan and is by disney.

I'm not quite sure how you could make defender 3d. The way the gameplay is setup it almost has to stay in that camera view. If not then you would have to change the entire gameplay mechanics and then it wouldn't be defender anymore. If you were referring to keeping the camera angle but rendering the ships in 3d, they have several defender clones out there that already do this.
As for a fps... bah!!! The modern pc is plagued with crappy fps games. They have been ran into the ground. Let id take care of them as they seem to be the only people to know how to do it right.
TMNT has gameplay mechanics that would translate well to 3d most of the other games you mentioned do not. Now if you are referring to the theme of the game then perhaps, but to translate any of those games to 3d wuld totally destroy the gameplay mechanics.
Why tmnt? Well first off the ninja turtles rule, everyone likes them (unless your an old stick in the mudd.) Secondly it's multi player which is always good for a 3d game and would make the translation more popular. Also the way tmnt was setup would translate very well to 3d. You just make a long rectangular polygon for the bounding mox and tilt it slightly forward to give you that 2 3/4 feel, but this time it would be in true 3d. The hit detection is extremely simple in this game as are the physics. A generic 3d game engine could be used to make this game with very little modification... simply make a fixed camera and your good to go. What would make it special would be the characters and the old-school gameplay.